The funny thing about heliocentrism is, that isn't really the modern view either. The modern view is that there are no privileged reference frames, and heliocentrism and geocentrisms are just questions of reference frame. You can construct consistent physical models from either, and for example, you'll probably use a geocentric model if you're gonna launch a satellite.
But another fun one is the so-called discovery of oxygen, which is really about what's going on with fire. Before Lavoisier, the dominant belief was that fire is the release of phlogiston. What discredited this was the discovery of materials that get heavier when burned.
Setting aside stuff like Plan Nine and Manos and The Room and Birdemic, probably Star Trek XI, the one that JJ made. Splicing together test footage of Bela Lugosi and his chiropractor is one thing, but desecrating something beautiful is a sin.